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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttgaacaatttccttgcctctattaaaatgtcaacatttactcattcaaacatgcttattgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA

Basic information

species Oryza sativa
transcript LOC_Os05g47545.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g47545.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G170400_T03 (Zea mays), 3'ss of exon 5
gtcagttgaacaatttccttgcct--ctattaaaatgtcaa-catttactc-attcaaa---catgct-tat-----tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA
|| ||   | ||||| ||||   |  ||  |||     ||| ||||||  | || || |   ||  || |||     | ||||||||| || ||||||||||||||||  | ||| ||||||||||| || |||||||| |||||||| || || |||||||||||||||||||| || ||||||| 
gtgagcccatcaattgcctttgtttactgctaactcaccaatcatttatgctatacatagatcacactgtatccgtttcatgaacagAGACTACAAAGGAATTTGTGGGCATGCTCGATCTTAAACCGGGCCAGAAAGTACTTGATGTCGGATGTGGAATTGGAGGCGGCGACTTTTACATGGCTGC

upper sequence: LOC_Os05g47545.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcagttgaaca--atttccttgcctctattaaaatgtcaacatttac------------tcattcaaacatgcttattga--tgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA
|| | |  |     | |   ||  ||  ||    |  |    | ||              | ||    |  | ||| ||    | |||||| || || || ||||||||||  ||| |||| |||||||| ||||||||||| || |||||||| || || || || || || |||||||| ||||||||
gtaattccattcttactcttttatcttcatatggacatacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA

upper sequence: LOC_Os05g47545.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G18000.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------gtcagttgaacaatttcct-tgcctctattaaaatgtcaacatttactcattcaaacatgcttattgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA
                     |   ||      || | || || ||  ||| |   ||  || | |     |||   | || || |||||   |||| || || || ||||||||||| ||  || |||| ||||| |||||||||||  | ||||||||||| || ||||| || || |||||||| ||||||||
gtaaaagctcaattcgatttcgcttgtgttgtgatgttctgtgtcttcatttagcagt--acttatgtgtgttctgtcgtgtttcttgat--tcagAGACAACCAAAGAATTTGTGGAGAAAATGAATCTGAAACCAGGACAGAAAGTCTTAGATGTTGGGTGTGGCATTGGTGGAGGTGACTTCTACATGGCTGA

upper sequence: LOC_Os05g47545.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G73600.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------------------------------gtcagttgaac--aatttccttgcctctattaaa--atgtcaacatttactcat-tcaaacatgcttattgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA
                                                    ||   |||||   || ||        | |||||   | |  | | |||  || | | | || || || ||     | ||| || ||||||||||| ||||||| ||||||||| |||||||| || ||||| || || |||||||||||||| ||||| || |||||||| ||||||||
gtatgctctttagtcatcgagtttgtatcaactttgcagtattgatggttctgttt-ttgaatttaagttatacagaaccattaagtgaagctatcttttcttcttattatacttgtttcttttgatatagAGACAACAAAGGAATTCGTGGATATGCTGGATCTGAAACCTGGCCAAAAAGTTCTAGACGTTGGGTGCGGAATAGGAGGAGGGGACTTCTACATGGCTGA

upper sequence: LOC_Os05g47545.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtcagttgaacaatttccttgcctctattaaaat---gtcaacatttact-cattcaaacatgcttattgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA
                      |  |  | |    |||  ||  || || |||| |    | | || ||  | || | | | |  |       ||| ||||||| |||||||||||||||| |||| |||| ||||| || || |||||||| || || || || || || ||||| || || |||||||| ||||||||
ctaagcacaaattgccattcatgagaaattattcgtttaattaactataataaattccaattaccaattcttgcactgagaaaatcccgaatttgatcagAAACAACAAAGGAATTTGTGGCTAAGTTGGAGCTTAAGCCCGGCCAGAAAGTCCTGGACGTAGGTTGTGGCATTGGCGGAGGTGACTTCTACATGGCTGA

upper sequence: LOC_Os05g47545.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv17s0000g02430.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------gtcagttgaacaatttccttgcctct--attaaaatgtcaacatttactcattcaaacatgcttattgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA
                            ||| |||||  |||   |  | | |  ||||  ||      | || ||  |      |  ||  |   ||| |||| || ||||| ||||||||||  || ||||| ||||||||||| ||||| || || ||||| || || || |||||||| || |||||||||||||| ||
cagataattattagctggttttcatgaatcatttgaa--attcagtgacttgttaattagtattcttctaatttctt-tgagtgaaccctggtctttgagcagAGACAACAAAAGAATTTGTGGGAAAACTGGACCTTAAACCTGGCCAGAAGGTCCTAGATGTGGGCTGTGGCATTGGAGGAGGTGACTTCTATATGGCAGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|163927904|gb|EG714248.1|EG714248
EST:     ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
genomic: ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
EST: gi|58598352|gb|CK008880.1|CK008880
EST:     ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
genomic: ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
EST: gi|163926700|gb|EG713716.1|EG713716
EST:     ACGCTATGGGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
genomic: ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
EST: gi|58598726|gb|CK009254.1|CK009254
EST:     ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
genomic: ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
EST: gi|58679178|gb|CK067865.1|CK067865
EST:     ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
genomic: ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
EST: gi|58682448|gb|CK071135.1|CK071135
EST:     ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
genomic: ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG
EST: gi|58677251|gb|CK065938.1|CK065938
EST:     ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATAAGCTGGATCTTA
genomic: ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTA
EST: gi|58673514|gb|CK062200.1|CK062200
EST:     CGCTATGAGCGTTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTTGGACAGAAA
genomic: CGCTATGAGCGT-GTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCT-GGACAGAAA
EST: gi|58604229|gb|CK014757.1|CK014757
EST:     ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTG                         AAACCACAAAGGAATTTGTGGATCAGCTGGATCTTAAACCTGGACAGAAAG
genomic: ACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 74 (downstream exon)
Score: 73

GGATTCCAAAGATTCCTGGACAATGTGCAGTACAAAACCACTGGAATCTTACGCTATGAGCGTGTCTTCGGAGAGGGTTATGTCAGCACTGGTGGAATTGgtcagttgaa ... tgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctctattaaaatgtcaacatttactcattcaaacatgcttattgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA
                                          tattgat  putative branch site (score: 73)
      tattaaaatgtcaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttgaacaatttccttgcctctattaaaatgtcaacatttactcattcaaacatgcttattgatgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG